@prefix LoadListingRequirement: .
@prefix SchemaDefRequirement: .
@prefix CommandLineBinding: .
@prefix EnvVarRequirement: .
@prefix xsd: .
@prefix DockerRequirement: .
@prefix Workflow: .
@prefix sld: .
@prefix CommandOutputBinding: .
@prefix ns1: .
@prefix NetworkAccess: .
@prefix rdf: .
@prefix EnvironmentDef: .
@prefix cwl: .
@prefix ResourceRequirement: .
@prefix ExpressionTool: .
cwl:source .
a cwl:File .
sld:fields , , ;
sld:type sld:record .
sld:type xsd:string .
sld:type xsd:string .
a cwl:Workflow ;
ns1:original_cwlVersion "v1.0" ;
Workflow:steps , ;
cwl:cwlVersion ;
cwl:hints [ a ;
NetworkAccess:networkAccess true
] ;
cwl:hints [ a ;
LoadListingRequirement:loadListing
"deep_listing"
] ;
cwl:inputs , ;
cwl:outputs ;
cwl:requirements [ a cwl:SchemaDefRequirement ;
SchemaDefRequirement:types , ,
] ;
cwl:requirements [ a cwl:InlineJavascriptRequirement ] ;
cwl:requirements [ a cwl:StepInputExpressionRequirement ] .
a cwl:ExpressionTool ;
ns1:original_cwlVersion "v1.0" ;
ExpressionTool:expression "${\n return {\"output\": {\"key\": inputs.file_key, \"file\": inputs.main_file}};\n }\n" ;
cwl:cwlVersion ;
cwl:hints [ a ;
NetworkAccess:networkAccess true
] ;
cwl:hints [ a ;
LoadListingRequirement:loadListing
"deep_listing"
] ;
cwl:inputs , ;
cwl:outputs ;
cwl:requirements [ a cwl:SchemaDefRequirement ;
SchemaDefRequirement:types , ,
] ;
cwl:requirements [ a cwl:InlineJavascriptRequirement ] .
sld:type xsd:string .
cwl:source ;
cwl:valueFrom "$(self.key)" .
sld:type cwl:File .
cwl:in , ;
cwl:out ;
cwl:run .
cwl:source .
cwl:default 1 ;
sld:type xsd:long .
cwl:inputBinding [ CommandLineBinding:position
98 ] ;
sld:type xsd:string .
cwl:inputBinding [ CommandLineBinding:position 0 ;
CommandLineBinding:prefix "-c"
] ;
sld:type cwl:File .
sld:fields , ;
sld:type sld:record .
sld:type xsd:string , sld:null .
cwl:default "download" ;
cwl:inputBinding [ CommandLineBinding:position
1 ] ;
sld:type xsd:string .
sld:type cwl:File .
sld:type .
sld:fields , ;
sld:type sld:record .
a cwl:CommandLineTool ;
ns1:original_cwlVersion "v1.0" ;
cwl:baseCommand ( "/usr/local/bin/bio_client.py" ) ;
cwl:cwlVersion ;
cwl:hints [ a ;
NetworkAccess:networkAccess true
] ;
cwl:hints [ a ;
LoadListingRequirement:loadListing
"deep_listing"
] ;
cwl:inputs , , , , , ;
cwl:outputs ;
cwl:requirements [ a cwl:ResourceRequirement ;
ResourceRequirement:coresMax 1 ;
ResourceRequirement:coresMin 1 ;
ResourceRequirement:outdirMax "$(Math.ceil (inputs.file_size / 1048576))" ;
ResourceRequirement:outdirMin "$(Math.ceil (inputs.file_size / 1048576))" ;
ResourceRequirement:ramMax 2000 ;
ResourceRequirement:ramMin 2000 ;
ResourceRequirement:tmpdirMax "$(Math.ceil (inputs.file_size / 1048576))" ;
ResourceRequirement:tmpdirMin "$(Math.ceil (inputs.file_size / 1048576))"
] ;
cwl:requirements [ a cwl:EnvVarRequirement ;
EnvVarRequirement:envDef [ EnvironmentDef:envName "REQUESTS_CA_BUNDLE" ;
EnvironmentDef:envValue "$(inputs.cert.path)"
]
] ;
cwl:requirements [ a cwl:DockerRequirement ;
DockerRequirement:dockerPull "{{ docker_repo }}/bio-client:{{ bio_client }}"
] ;
cwl:requirements [ a cwl:InlineJavascriptRequirement ] .
cwl:outputSource ;
sld:type .
sld:type xsd:string .
cwl:source ;
cwl:valueFrom "$(self.uuid)" .
cwl:default "." ;
cwl:inputBinding [ CommandLineBinding:position 99 ;
CommandLineBinding:prefix "--dir_path"
] ;
sld:type xsd:string .
sld:type cwl:File .
sld:type xsd:string .
sld:type .
cwl:default ;
sld:type cwl:File .
sld:type xsd:string .
cwl:in , ;
cwl:out ;
cwl:run .
cwl:outputBinding [ CommandOutputBinding:glob
"*" ] ;
sld:type cwl:File .